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Conserved domains on  [gi|6323745|ref|NP_013816|]
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Atp25p [Saccharomyces cerevisiae S288C]

Protein Classification

RsfS and mRNA_stabil domain-containing protein( domain architecture ID 10493356)

RsfS and mRNA_stabil domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
mRNA_stabil super family cl16483
mRNA stabilization; This domain is an mRNA stabilization factor.
306-594 6.69e-102

mRNA stabilization; This domain is an mRNA stabilization factor.


The actual alignment was detected with superfamily member pfam13929:

Pssm-ID: 433586  Cd Length: 286  Bit Score: 310.81  E-value: 6.69e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    306 FLQKEDFKGANKIIQSSSgtETHNIRTLEHVKNTLKDLVGQERKVDVVQWKSLFDEHSTFLTINQSAAYWPLRLEYAILL 385
Cdd:pfam13929   3 ALSKQDFDSALKLLQSNK--EENSLDPLKSIVDTLSQLPSQEKEVDIENWKKFFDSHWPLVIPSDSSKYWSLRLKFLKLL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    386 NKADPQFYSDRVFLKDYLLLKKSLGQELIREDLIALLEMVLKTQHSSHSYFNLVKQNRVIIRALNLFKGLqtedDGSVVY 465
Cdd:pfam13929  81 NIANPQAYSLRRFFKDYLLLKKSMGFELTKEDLIGFLKIVITNLNLSANYWDLVKRNRVVVEALQLYDDL----DPSIIH 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    466 DEVVISLLLNSMVADERV-KLRSLYETIDHIFQTFGDKLTSGMIVSILQNLAKIKDWNKLLQVWEAITPTEGEGQDKRPW 544
Cdd:pfam13929 157 DEQVISLLLKTMITDDRKhKLNSLYEVVDYLVDTFGGELTPTVIISILETLAEAKDWDKLFQFWETCIALASPDSDTRPW 236
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 6323745    545 NEFINVINQSGDSHVISKIVNNGHLLWIRRLNVNVTPELCNSIKALLKTA 594
Cdd:pfam13929 237 AEFIKLINASGDLELIRKIIDDGHLLWLKRNNVPITPELRDQLSKLFERV 286
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
105-246 4.01e-16

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


:

Pssm-ID: 460550  Cd Length: 97  Bit Score: 74.02  E-value: 4.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    105 RKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKHCHKSFLELNKFLKHEFCSSAYVEGNFNERqe 184
Cdd:pfam02410   1 ELIAEALDDKKA-EDIVVLDVRGKSS--------IADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGD-- 69
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6323745    185 srrkrrlarksnlskllgrssecsakdlnseaWYMIDCrvDGIFVNILTQRRRNELNLEELY 246
Cdd:pfam02410  70 --------------------------------WVLLDY--GDVVVHIFTPEAREFYNLERLW 97
 
Name Accession Description Interval E-value
mRNA_stabil pfam13929
mRNA stabilization; This domain is an mRNA stabilization factor.
306-594 6.69e-102

mRNA stabilization; This domain is an mRNA stabilization factor.


Pssm-ID: 433586  Cd Length: 286  Bit Score: 310.81  E-value: 6.69e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    306 FLQKEDFKGANKIIQSSSgtETHNIRTLEHVKNTLKDLVGQERKVDVVQWKSLFDEHSTFLTINQSAAYWPLRLEYAILL 385
Cdd:pfam13929   3 ALSKQDFDSALKLLQSNK--EENSLDPLKSIVDTLSQLPSQEKEVDIENWKKFFDSHWPLVIPSDSSKYWSLRLKFLKLL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    386 NKADPQFYSDRVFLKDYLLLKKSLGQELIREDLIALLEMVLKTQHSSHSYFNLVKQNRVIIRALNLFKGLqtedDGSVVY 465
Cdd:pfam13929  81 NIANPQAYSLRRFFKDYLLLKKSMGFELTKEDLIGFLKIVITNLNLSANYWDLVKRNRVVVEALQLYDDL----DPSIIH 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    466 DEVVISLLLNSMVADERV-KLRSLYETIDHIFQTFGDKLTSGMIVSILQNLAKIKDWNKLLQVWEAITPTEGEGQDKRPW 544
Cdd:pfam13929 157 DEQVISLLLKTMITDDRKhKLNSLYEVVDYLVDTFGGELTPTVIISILETLAEAKDWDKLFQFWETCIALASPDSDTRPW 236
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 6323745    545 NEFINVINQSGDSHVISKIVNNGHLLWIRRLNVNVTPELCNSIKALLKTA 594
Cdd:pfam13929 237 AEFIKLINASGDLELIRKIIDDGHLLWLKRNNVPITPELRDQLSKLFERV 286
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
105-246 4.01e-16

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


Pssm-ID: 460550  Cd Length: 97  Bit Score: 74.02  E-value: 4.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    105 RKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKHCHKSFLELNKFLKHEFCSSAYVEGNFNERqe 184
Cdd:pfam02410   1 ELIAEALDDKKA-EDIVVLDVRGKSS--------IADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGD-- 69
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6323745    185 srrkrrlarksnlskllgrssecsakdlnseaWYMIDCrvDGIFVNILTQRRRNELNLEELY 246
Cdd:pfam02410  70 --------------------------------WVLLDY--GDVVVHIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
104-153 8.80e-05

Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440562  Cd Length: 113  Bit Score: 42.03  E-value: 8.80e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6323745  104 LRKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKH 153
Cdd:COG0799   9 LKLIAKALDDKKA-EDIVVLDVRGLSS--------IADYFVIASGTSDRQ 49
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
104-153 4.88e-04

ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. [Protein synthesis, Translation factors]


Pssm-ID: 272901  Cd Length: 99  Bit Score: 39.75  E-value: 4.88e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 6323745    104 LRKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKH 153
Cdd:TIGR00090   2 LELIVEALDDKKA-EDIVVLDVRGKSS--------IADYFVIASGTSSRH 42
 
Name Accession Description Interval E-value
mRNA_stabil pfam13929
mRNA stabilization; This domain is an mRNA stabilization factor.
306-594 6.69e-102

mRNA stabilization; This domain is an mRNA stabilization factor.


Pssm-ID: 433586  Cd Length: 286  Bit Score: 310.81  E-value: 6.69e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    306 FLQKEDFKGANKIIQSSSgtETHNIRTLEHVKNTLKDLVGQERKVDVVQWKSLFDEHSTFLTINQSAAYWPLRLEYAILL 385
Cdd:pfam13929   3 ALSKQDFDSALKLLQSNK--EENSLDPLKSIVDTLSQLPSQEKEVDIENWKKFFDSHWPLVIPSDSSKYWSLRLKFLKLL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    386 NKADPQFYSDRVFLKDYLLLKKSLGQELIREDLIALLEMVLKTQHSSHSYFNLVKQNRVIIRALNLFKGLqtedDGSVVY 465
Cdd:pfam13929  81 NIANPQAYSLRRFFKDYLLLKKSMGFELTKEDLIGFLKIVITNLNLSANYWDLVKRNRVVVEALQLYDDL----DPSIIH 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    466 DEVVISLLLNSMVADERV-KLRSLYETIDHIFQTFGDKLTSGMIVSILQNLAKIKDWNKLLQVWEAITPTEGEGQDKRPW 544
Cdd:pfam13929 157 DEQVISLLLKTMITDDRKhKLNSLYEVVDYLVDTFGGELTPTVIISILETLAEAKDWDKLFQFWETCIALASPDSDTRPW 236
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 6323745    545 NEFINVINQSGDSHVISKIVNNGHLLWIRRLNVNVTPELCNSIKALLKTA 594
Cdd:pfam13929 237 AEFIKLINASGDLELIRKIIDDGHLLWLKRNNVPITPELRDQLSKLFERV 286
RsfS pfam02410
Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial ...
105-246 4.01e-16

Ribosomal silencing factor during starvation; This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases.


Pssm-ID: 460550  Cd Length: 97  Bit Score: 74.02  E-value: 4.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323745    105 RKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKHCHKSFLELNKFLKHEFCSSAYVEGNFNERqe 184
Cdd:pfam02410   1 ELIAEALDDKKA-EDIVVLDVRGKSS--------IADYFVIATGTSERHVRAIADEVEEKLKEAGGKPLRIEGLREGD-- 69
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6323745    185 srrkrrlarksnlskllgrssecsakdlnseaWYMIDCrvDGIFVNILTQRRRNELNLEELY 246
Cdd:pfam02410  70 --------------------------------WVLLDY--GDVVVHIFTPEAREFYNLERLW 97
RsfS COG0799
Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ...
104-153 8.80e-05

Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440562  Cd Length: 113  Bit Score: 42.03  E-value: 8.80e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6323745  104 LRKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKH 153
Cdd:COG0799   9 LKLIAKALDDKKA-EDIVVLDVRGLSS--------IADYFVIASGTSDRQ 49
rsfS_iojap_ybeB TIGR00090
ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of ...
104-153 4.88e-04

ribosome silencing factor RsfS/YbeB/iojap; This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. [Protein synthesis, Translation factors]


Pssm-ID: 272901  Cd Length: 99  Bit Score: 39.75  E-value: 4.88e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 6323745    104 LRKIADLLTGKLGlDDFLVFDLRKKSPnsvsavnkLGDFMVICTARSTKH 153
Cdd:TIGR00090   2 LELIVEALDDKKA-EDIVVLDVRGKSS--------IADYFVIASGTSSRH 42
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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